FRETboard: Semisupervised classification of FRET traces

Förster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nanoscale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner but lack the flexibility to adapt to different experimental setups and require local installations. Here, we propose to fit models to optical signals more intuitively by adopting a semisupervised approach, in which the user interactively guides the model to fit a given data set, and introduce FRETboard, a web tool that allows users to provide such guidance. We show that our approach is able to closely reproduce ground truth FRET statistics in a wide range of simulated single-molecule scenarios and correctly estimate parameters for up to 11 states. On in vitro data, we retrieve parameters identical to those obtained by laborious manual classification in a fraction of the required time. Moreover, we designed FRETboard to be easily extendable to other models, allowing it to adapt to future developments in FRET measurement and analysis.     

Cloning of DNA segments of phage 2C, which allows autonomous plasmid replication in Bacillus subtilis

The chromosome of Bacillus subtilis phage 2C is a 100-MDa double-stranded DNA molecule, containing hydroxymethyluracil in place of thymine and carrying redundant ends each encompassing 10% of the genome. 2C DNA was cleaved with EcoRI and HindIII, and cloned in the shuttle plasmids pSC 540 and pCP 115, both containing segments originating from B. subtilis and Escherichia coli plasmids. These chimaerical plasmids, carrying the chloramphenicol resistance gene, were unable to replicate in B. subtilis; this ability was restored, however, after the insertion of viral DNA segments. Physical maps of the recombinant plasmids were made; a large deletion of the E. coli-derived segment of pSC 540 was observed (which paralleled a loss of replication in this host), whereas addition of 2C DNA segments in pCP 115 was not accompanied by deletion (replication in E. coli was conserved in this case). Cloned viral segments mapped mostly, but not exclusively, within the redundant ends of 2C DNA. It is suggested that the thirteen recombinant clones carried the replication origin region of phage 2C DNA, and that these sequences originated within or close to the redundant extremities of the viral chromosome.     

The MDR1 gene product, P-glycoprotein, mediates the transport of the cardiac glycoside, digoxin.

Digoxin, a widely used cardiac glycoside with a low therapeutic index, is known to interact with a large and diverse group of co-administered drugs, frequently leading to toxic accumulation of the glycoside. Establishing the mechanism(s) of these interactions, therefore, has potential clinical significance. The present studies implicate P-glycoprotein, the MDR1 gene product overexpressed in multidrug resistant cells, as the apical membrane protein responsible for the renal secretion of digoxin and provide an explanation for the occurrence of digoxin toxicity in the presence of certain co-administered medications. Since digoxin is considered a prototype for endogenous digitalis-like glycosides, the results also allow for speculation that endogenous digitalis-like glycosides may be the natural substrates for P-gp.     

In vivo induction of P‐glycoprotein expression at the mouse blood–brain barrier: an intracerebral microdialysis study

Intracerebral microdialysis was utilized to investigate the effect of P‐glycoprotein (a drug efflux transporter) induction at the mouse blood–brain barrier (BBB) on brain extracellular fluid concentrations of quinidine, an established substrate of P‐glycoprotein. Induction was achieved by treating male CD‐1 mice for 3 days with 5 mg/kg/day dexamethasone (DEX), a ligand of the nuclear receptor, pregnane X receptor, and a P‐glycoprotein inducer. Tandem liquid chromatography mass spectrometric method was used to quantify analytes in dialysate, blood and plasma. P‐glycoprotein, pregnane X receptor and Cyp3a11 (metabolizing enzyme for quinidine) protein expression in capillaries and brain homogenates was measured by immunoblot analysis. Following quinidine i.v. administration, the average ratio of unbound quinidine concentrations in brain extracellular fluid (determined from dialysate samples) to plasma at steady state (375–495 min) or K_{p, uu, ECF/Plasma} in the DEX‐treated animals was 2.5‐fold lower compared with vehicle‐treated animals. In DEX‐treated animals, P‐glycoprotein expression in brain capillaries was 1.5‐fold higher compared with vehicle‐treated animals while Cyp3a11 expression in brain capillaries was not significantly different between the two groups. These data demonstrate that P‐gp induction mediated by DEX at the BBB can significantly reduce quinidine brain extracellular fluid concentrations by decreasing its brain permeability and further suggest that drug–drug interactions as a result of P‐gp induction at the BBB are possible.

     

Zur Prägung von Instinkthandlungen (Untersuchungen an Stockenten Anas platyrhynchos L. und Kolbenenten Netta rufina Pallas)

Ziel dieser Arbeit ist es, zu untersuchen, a) wie die durch Prägung auf ein Objekt gerichteten artspezifischen Instinktbewegungen sich an dieses an-passen, b) ob andere Einflüsse als die Prägung zu demselben Ergebnis in der Arterkennung führen können. Die Ausdrucksbewegungen und die Paarbildung der Stockente Anas platyrhynchos L. und der Kolbenente Netta rufina Pallas werden untersucht bei Tieren, die 1. mit Artgenossen, 2. mit Fremdgenossen, 3. unter Prägungsbedingungen, 4. erst mit Art-, dann mit Fremdgenossen, 5. als Kaspar-Hauser, aufgezogen wurden.

• 1 Sowohl hinsichtlich der Ontogenese wie der Bedingungen ihres Auftretens bleiben diese Bewegungen gleich, ob die Enten sie nun auf Artgenossen oder auf Fremdgenossen richten.
• 2 Die Prägung bestimmt die Taxis-Komponente der Instinktbewegung.
• 3 Zwischen auf Fremdgenossen geprägten Enten erscheinen Wechselwirkungen zwischen Sätzen von Instinktbewegungen; einige von ihnen drücken Verwechslungen formähnlicher Bewegungen aus. Die Bildung sozialer Bezie-hungen unter geprägten Enten kann zur Häufung nicht-arttypischer Ausdrucksbewegungen führen.
• 3 Die aggressiven Bewegungen werden sowohl auf Fremd- wie auch auf Artgenossen gerichtet. In der Paarbildung ist die Rivalität der ♂♂ untereinander wichtiger als ihre Artzugehörigkeit.
• 4 Die Beobachtungen machen wahrscheinlich, daß die Arterkennung bei den untersuchten Enten vor allem auf selektivem Lernen bestimmter Merk-male beruht.

Sowohl in Bezug auf die Nachfolgereaktion als auch auf die sexuelle Prägung werden die Prägungsmerkmale erörtert und der Begriff neu definiert, da anscheinend allein die ?primacy of experience” die Prägung im Gegensatz zu anderen Lernarten kennzeichnet.     

Bifunctional activity of transforming growth factor type beta on the growth of NRK-49F cells, normal and transformed by Kirsten murine sarcoma virus

Transformation of rat NRK-49F cells (49F) by Kirsten murine sarcoma virus (Ki-MSV) renders these cells (Ki-49F cells) capable of autonomous anchorage independent (AI) growth. As compared to nontransformed 49F cells, the transformation by Ki-MSV does not modify the cell response to transforming growth factor-beta (TGF-beta) in monolayer conditions, but alters it in A I growth conditions. The growth of nontransformed or Ki-MSV-transformed adherent 49F cells is slowed down by porcine TGF-beta, and this effect is reversed by epidermal growth factor (EGF). This decrease in the cell growth rate, induced by TGF-beta, does not affect the cloning efficiency of untransformed and transformed adherent 49F cells. Contrarily, porcine TGF-beta decreases the A I cloning efficiency of Ki-49F cells in agar-gelled medium; this effect is only partly reversed by EGF, which does not synergise with TGF-beta to enhance the A I growth as in the case of untransformed 49F cells. Media conditioned by 49F cells, Ki-49F cells, and chicken embryo fibroblasts contain a latent TGF-beta whose capacity to promote the A I growth of 49F cells and to inhibit that of Ki-49F cells is unmasked by acidification. The same situation exists concerning TGF-beta from human platelets. Neutral extracts are inefficient in both tests of promotion and inhibition of A I growth and contain an acid-activable component with an apparent molecular weight of 600 kd. In acid extracts, a 5-9 kd apparent molecular weight component is responsible for the A I growth enhancement of 49F cells and the A I growth inhibition of Ki-49F cells. Further purification by reverse phase chromatography shows that both activities strictly coelute at the same point (32%) of an acetonitrile gradient. These results indicate that TGF-beta is present in physiological conditions as a latent form which requires activation for inhibiting the A I growth of transformed cells as well as for enhancing that of 49F cells.     

Novel germline mutations in the APC gene and their phenotypic spectrum in familial adenomatous polyposis kindreds

Among 23 germline mutations identified in the APC screening of 45 familial adenomatous polyposis (FAP) patients, we have found 10 different novel frameshift mutations in 11 apparently unrelated patients. In two cases, an additional missense mutation was detected. One previously described as a causative germline mutation (S2621C), associated with a 1-bp insertion (4684insA) on the opposite allele, did not segregate with the FAP phenotype in the family and was therefore considered as being non-pathogenic. The other (Z1625H) was located 2 codons before a 1-bp deletion (4897delC). Both mutations were transmitted together from an FAP father to his affected son. The FAP phenotype of these 10 novel truncating mutations was clinically documented within their kindreds. Important variability was observed in the phenotype. Interestingly, we noted that a mutation (487insT) localized at the boundary of the 5’ attenuated APC phenotype region in two unrelated families resulted in classical polyposis. A clear-cut genotype-phenotype correlation could be drawn in only two instances. In one family, a 4684insA mutation led to a mild polyposis associated with early inherited osteomas and, in the family bearing the double mutation (Z1625H+4897delC), the phenotype was obviously a 3′ attenuated type. Our data illustrate the wide genetic and phenotypic heterogeneity of this condition between and within the families, making the establishment of correlations complex and any prediction in this disease difficult, although targeting the mutation site may be helpful in some specific cases. Received: 11 February 1997 / Accepted: 11 April 1997     

Consequences of ChemR23 Heteromerization with the Chemokine Receptors CXCR4 and CCR7

Recent studies have shown that heteromerization of the chemokine receptors CCR2, CCR5 and CXCR4 is associated to negative binding cooperativity. In the present study, we build on these previous results, and investigate the consequences of chemokine receptor heteromerization with ChemR23, the receptor of chemerin, a leukocyte chemoattractant protein structurally unrelated to chemokines. We show, using BRET and HTRF assays, that ChemR23 forms homomers, and provide data suggesting that ChemR23 also forms heteromers with the chemokine receptors CCR7 and CXCR4. As previously described for other chemokine receptor heteromers, negative binding cooperativity was detected between ChemR23 and chemokine receptors, i.e. the ligands of one receptor competed for the binding of a specific tracer of the other. We also showed, using mouse bone marrow-derived dendritic cells prepared from wild-type and ChemR23 knockout mice, that ChemR23-specific ligands cross-inhibited CXCL12 binding on CXCR4 in a ChemR23-dependent manner, supporting the relevance of the ChemR23/CXCR4 interaction in native leukocytes. Finally, and in contrast to the situation encountered for other previously characterized CXCR4 heteromers, we showed that the CXCR4-specific antagonist AMD3100 did not cross-inhibit chemerin binding in cells co-expressing ChemR23 and CXCR4, demonstrating that cross-regulation by AMD3100 depends on the nature of receptor partners with which CXCR4 is co-expressed.